Transcriptome profiling was conducted to detect genes whose expression is significantly changed in an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1) during early seedling development when mutant phenotypes could be clearly observed. A total of 2040 differentially expressed genes were identified, representing approximately 6.7% of the total DNA oligonucleotide targets of 30385 on the microarray. Among these differential expressed genes, many were mapped to pathways essential to plant growth and development including those of primary, secondary and hormone metabolisms. A significant proportion of up-regulated genes encoded transposable elements which were mapped to the centromeric and pericentromeric regions of the Arabidopsis chromosomes. A number of down-regulated genes were found to be involved in root hair formation, which might have contributed to the root hair defective phenotype of the mutant. Despite SAHH1 deficient, the expression of genes encoding methyltransferase remained largely unchanged in the sahh1 mutant. Analysis of mutant transposable elements (TE) suggested a genome-wide hypomethylation had occurred. These results indicated that SAHH1 might play a critical role in methyl homeostasis, and its deficiency is a major contributing factor to the change of global gene expression, metabolic pathways and activation of transposons in the sahh1 mutant.